mcroastyx: Multiple Contrast Rotation Tests

Description Usage Arguments Details Value Author(s) References

Description

Adaption of the roast function in package limma to perform a maxT-test in the multivariate linear model, controlling FWER for multiple contrasts.

Usage

1
mcroastyx(Y, X, K, nrot = 9999, adjusted = TRUE, moderated = FALSE)

Arguments

Y

A matrix of response variables with individuals in rows and responses in columns

X

A design matrix with the same number of rows as Y

K

A contrast matrix, with different contrasts in rows, and the same number of columns as X

nrot

Number of Monte Carlo simulation steps

adjusted

logical, if TRUE single-step maxT FWER control is performed; if FALSE the comparison-wise error rate is controlled

moderated

logical, if TRUE, moderated statistics (Smyth 2004) are used.

Details

Most of the code was taken from function roast in package limma (Bioconductor).

Value

A list with

Y

The matrix of response variables

X

The design matrix

statistic

A matrix of test statistics

pvalue

A matrix of (adjusted) p-values

B

A matrix with contrast parameter estimates

SD

A matrix with estimated standard deviations

mrot

A vector with simulated maxT statistics under H0

Author(s)

Daniel Gerhard

References

Wu, D, Lim, E, Francois Vaillant, F, Asselin-Labat, M-L, Visvader, JE, and Smyth, GK (2010). ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics 26, 2176-2182.

Langsrud, O (2005). Rotation tests. Statistics and Computing 15, 53-60.


daniel-gerhard/mcroast documentation built on May 14, 2019, 3:38 p.m.